Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

Science. 2015 Sep 4;349(6252):1101-1106. doi: 10.1126/science.aac4812. Epub 2015 Jul 30.

Abstract

Metagenomic sequencing increased our understanding of the role of the microbiome in health and disease, yet it only provides a snapshot of a highly dynamic ecosystem. Here, we show that the pattern of metagenomic sequencing read coverage for different microbial genomes contains a single trough and a single peak, the latter coinciding with the bacterial origin of replication. Furthermore, the ratio of sequencing coverage between the peak and trough provides a quantitative measure of a species' growth rate. We demonstrate this in vitro and in vivo, under different growth conditions, and in complex bacterial communities. For several bacterial species, peak-to-trough coverage ratios, but not relative abundances, correlated with the manifestation of inflammatory bowel disease and type II diabetes.

Trial registration: ClinicalTrials.gov NCT01892956.

Publication types

  • Clinical Trial
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / classification
  • Bacteria / genetics
  • Bacteria / growth & development*
  • Diabetes Mellitus, Type 2 / microbiology*
  • Gastrointestinal Tract / microbiology*
  • Genome, Bacterial
  • Humans
  • Inflammatory Bowel Diseases / microbiology*
  • Metagenome
  • Metagenomics
  • Microbiota / genetics
  • Microbiota / physiology*

Associated data

  • ClinicalTrials.gov/NCT01892956